I mean, the first time I went to Japan (and again after I moved there) I was surprised how much it looked like it did in anime. Unlike most American cartoons, anime draws heavy inspiration from real-life settings, either generally or by literally copying real places almost exactly (there were places in Tokyo I stumbled across and went "wait this actually exists?!"). Furthermore a lot of the daily minutia commonly depicted in anime is true to life: late-night walks to the convenience store, kids biking to school, exhausted salarymen taking the last train, housewives gossiping on the streetcorner, strangely perky cashiers... Also anime usually shows families living in pretty standard housing, and many are set in cheap studio apartments that are quite accurate. They often show how over-worked and despairing both students and working adults are. They often incorporate hot-button issues, like bullying, the high suicide rate, and rural depopulation, that are usually at least generally accurate.

I guess I'm not sure what you're getting at specifically. Yes anime is disproportionately set in Tokyo, but Japan as a whole is disproportionately focused around Tokyo (culturally, economically, and physically, since the Kanto plain is one of the only flat areas large enough to handle urban sprawl), and it's not like other places are never featured (often the non-Tokyo setting is a major element of the story). Compared to American TV/movies/cartoons, I've found Japanese media to be quite true to life.